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Table 2 List of 90 significantly enriched human pathways in the meta-analysis

From: Meta-analysis of human gene expression in response to Mycobacterium tuberculosis infection reveals potential therapeutic targets

Map

Major Process

- log (P)

DEGs

In dendritic data

In THP-1 data

Attenuation of IFN type I signaling in melanoma cells

Cancer

8.53

17

Y

N

Bacterial infections in CF airways

CF pathways

7.66

18

N

Y

Role of PKR in stress-induced antiviral cell response

Immune response

6.41

18

Y

Y

B cell signaling in hematological malignancies

Immune response

6.29

21

N

N

Bacterial infections in normal airways

Immune response

5.93

16

N

N

TLR2 and TLR4 signaling pathways

Immune response

5.82

17

N

Y

Role of CD8+ Tc1 cells in COPD

COPD

4.95

14

Y

Y

SLE genetic marker-specific pathways in B cells

Immune response

4.74

21

N

Y

Release of pro-inflammatory mediators and elastolytic enzymes by alveolar macrophages in COPD

COPD

4.7

11

N

Y

G-CSF-induced myeloid differentiation

Development

4.43

11

N

Y

Inter-cellular relations in COPD (general schema)

COPD

4.43

11

Y

Y

IL-1 signaling pathway

Immune response

4.28

13

N

Y

Inflammatory mechanisms of pancreatic cancerogenesis

Cancer

4.25

16

Y

Y

Antiviral actions of Interferons

Immune response

4.25

14

N

N

Role of fibroblasts and keratinocytes in the elicitation phase of allergic contact dermatitis

Dermatitis

4.25

10

Y

Y

Inhibitory PD-1 signaling in T cells

Immune response

4.19

14

Y

N

Role of iNKT and B cells in T cell recruitment in allergic contact dermatitis

Dermatitis

4.07

12

N

N

LRRK2 and immune function in Parkinson’s disease

Parkinson

4.03

9

N

N

TLR5, TLR7, TLR8 and TLR9 signaling pathways

Immune response

4.03

13

N

Y

Chemokines in inflammation in adipose tissue and liver in obesity, type 2 diabetes and metabolic syndrome X

Immune response

4.03

13

N

Y

Neutrophil-derived granule proteins and cytokines in asthma

Asthma

3.94

13

N

N

Cigarette smoke-mediated attenuation of antibacterial and antivirus immune response

Immune response

3.92

10

Y

Y

Prostate Cancer: candidate susceptibility genes in inflammatory pathways

Cancer

3.92

10

N

N

Inhibition of apoptosis in multiple myeloma

Cancer

3.86

11

Y

N

SLE genetic marker-specific pathways in antigen-presenting cells (APC)

Immune response

3.79

17

Y

Y

Proinflammatory cytokine production by Th17 cells in asthma

Asthma

3.61

13

N

N

Antigen presentation by MHC class I, classical pathway

Immune response

3.53

13

Y

N

NK cells in allergic contact dermatitis

Dermatitis

3.43

10

N

Y

Inflammatory response in ischemia-reperfusion injury during myocardial infarction

Stem cells

3.36

8

N

Y

Putative pathways of activation of classical complement system in major depressive disorder

Complement activation

3.25

9

N

N

Th1 and Th17 cells in an autoimmune mechanism of emphysema formation in smokers

Signal transduction

3.25

9

N

Y

NF-kB activation pathways

Signal transduction

3.14

12

N

Y

iNKT cell-keratinocyte interactions in allergic contact dermatitis

Dermatitis

3.13

10

N

N

Apo-2 L(TNFSF10)-induced apoptosis in melanoma

Cancer

2.98

11

Y

Y

IFN alpha/beta signaling pathway

Immune response

2.95

8

Y

N

EGFR signaling pathway

Development

2.95

14

N

Y

Th17 cells in CF

CF pathways

2.95

12

N

N

ERBB family and HGF signaling in gastric cancer

Cancer

2.95

12

N

Y

Interleukins-induced inflammatory signaling in normal and asthmatic airway epithelium

Immune response

2.95

9

N

N

Role of keratinocytes and Langerhans cells in skin sensitization

Skin sensitization

2.87

8

N

N

Transcription regulation of granulocyte development

Development

2.87

9

N

Y

The role of KEAP1/NRF2 pathway in skin sensitization

Skin sensitization

2.87

9

N

Y

Activation of ACTH production in pituitary gland in major depressive disorder

Signal transduction

2.87

9

N

N

IFN gamma signaling pathway

Immune response

2.84

12

N

Y

Memory CD8+ T cells in allergic contact dermatitis

Dermatitis

2.84

10

N

Y

MIF in innate immunity response

Immune response

2.84

10

N

N

The innate immune response to contact allergens

Immune response

2.81

9

N

N

IL-5 signaling via JAK/STAT

Immune response

2.81

12

Y

Y

Cytokine-mediated regulation of megakaryopoiesis

Development

2.81

12

Y

N

Inflammasome in inflammatory response

Immune response

2.72

9

N

N

TLR ligands

Immune response

2.72

9

N

N

Rheumatoid arthritis (general schema)

Others

2.71

11

Y

N

Apoptotic TNF-family pathways

Apoptosis and survival

2.7

10

Y

N

Neutrophil resistance to apoptosis in COPD and proresolving impact of lipid mediators

COPD

2.64

12

Y

Y

Regulation of proinflammatory cytokine production by Th2 cells in asthma

Asthma

2.64

10

N

N

Role of cell adhesion in vaso-occlusion in Sickle cell disease

Sickle cell disease

2.64

10

N

N

Release of pro-inflammatory factors and proteases by alveolar macrophages in asthma

Asthma

2.64

10

Y

Y

HMGB1/TLR signaling pathway

Immune response

2.57

9

N

Y

Role of TLR signaling in skin sensitization

Skin sensitization

2.57

10

N

Y

Inhibition of neutrophil migration by proresolving lipid mediators in COPD

COPD

2.54

13

N

N

Role of PKR in stress-induced apoptosis

Apoptosis and survival

2.54

11

Y

N

TLRs-mediated IFN-alpha production by plasmacytoid dendritic cells in SLE

SLE

2.54

11

N

Y

Role of IFN-beta in activation of T cell apoptosis in multiple sclerosis

Multiple sclerosis

2.54

8

Y

N

HSP60 and HSP70/ TLR signaling pathway

Immune response

2.48

11

N

Y

T cell receptor signaling pathway

Immune response

2.41

11

N

N

Integrin inside-out signaling in T cells

Cell adhesion

2.39

13

Y

N

HGF signaling pathway

Development

2.37

10

Y

N

Prolactin/ JAK2 signaling in breast cancer

Cancer

2.32

7

N

Y

IFN-gamma and Th2 cytokines-induced inflammatory signaling in normal and asthmatic airway epithelium

Asthma

2.26

9

N

Y

TNF-alpha and IL-1 beta-mediated regulation of contraction and secretion of inflammatory factors in normal and asthmatic airway smooth muscle

Asthma

2.26

12

N

Y

Antigen presentation by MHC class II

Immune response

2.26

5

N

N

Integrin inside-out signaling in neutrophils

Cell adhesion

2.26

13

N

N

Role of B cells in SLE

SLE

2.26

11

Y

N

Th17 cells in CF (mouse model)

CF pathways

2.26

10

N

N

LPS-induced platelet activation

Immune response

2.24

7

N

N

IL-18 signaling

Immune response

2.15

11

N

Y

Inhibition of apoptosis in gastric cancer

Cancer

2.15

9

Y

Y

CD8+ Tc1 cells in allergic contact dermatitis

Dermatitis

2.15

7

Y

N

Role of IL-8 in colorectal cancer

Cancer

2.15

6

N

N

Schema: Initiation of T cell recruitment in allergic contact dermatitis

Dermatitis

2.15

6

N

N

Inhibition of WNT5A-dependent non-canonical pathway in colorectal cancer

Cancer

2.15

6

N

Y

Function of MEF2 in T lymphocytes

Immune response

2.15

10

N

Y

Caspase cascade

Apoptosis and survival

2.15

8

Y

Y

Regulation of Tissue factor signaling in cancer

Cancer

2.1

9

N

N

Regulatory T cells in murine model of contact hypersensitivity

Others

2.07

7

N

N

Production and activation of TGF-beta in airway smooth muscle cells

Signal transduction

2.07

8

N

N

Development_Growth hormone signaling via STATs and PLC/IP3

Development

2.07

8

N

Y

Apoptotic pathways and resistance to apoptosis in lung cancer cells

Cancer

2.04

10

Y

Y

Cigarette smoke-induced inflammatory signaling in airway epithelial cells

Signal transduction

2

8

N

Y

IL-12-induced IFN-gamma production

Immune response

2

8

N

N

  1. List of 90 significantly enriched human pathways in the meta-analysis, their major processes, −log (P-value), number of DEGs in the pathways, and whether they were identified in in vitro dendritic or THP-1 datasets